How to represent and work with the feature matrix for graph convolutional network (GCN) if the number of features for each node is different?
The simplest way I could come with is to pad with 0 each feature which is not present. You said that you're going to add too much noise to the network, but I don't see the problem (please correct me if I'm wrong). For example we have two nodes, the first one has only 2 features with the 3rd one missing and the second node has all features X=[[1,2,0], [3,4,5]]. Now we can project the nodes to a hidden representation (pretty common). I'm going to use a weight matrix of W=[[1], [1], [1]]. The output of XW will be [[3], [12]]. Now let's add a new feature to the second node X=[[1,2,0, 0], [3,4,5,6]] and apply the same transformation W=[[1], [1], [1], [1]] the output will be [[3], [18]] you can see that the first node is not affected by the number of missing features. 

Another way you could achieve this if you don't want to use the projection could be using a mask. For example give the same example above we could create a mask M=[[1,1,0], [1,1,1]] where each entry represents if a specific feature is present in a specific node. Now usually a GCN layer is defined as H=f(AHW) where A is the adjacency matrix. We could change the propagation rule to H=f(AH*MW) where * is the pointwise multiplication. Like this if a node is missing a feature it can not "access" information from others that are having that feature.